Health benefits of soybean germ oil have not yet been fully explored. The present study examined the blood cholesterol-lowering activity of soybean germ oil and the underlying mechanisms in hypercholesterolemic hamsters. Forty hamsters were randomly assigned into five groups and fed a non-cholesterol diet, a high cholesterol diet and one of three high cholesterol diets containing 0.50% cholestyramine, 4.75% soybean germ oil, and 9.50% soybean germ oil, respectively, for 6 weeks. The result showed that soybean germ oil significantly decreased plasma cholesterol by 18.5–31.5%, which was accompanied by 28.3–62.7% increase in excretion of fecal neutral sterols and bile acids. The effect was mediated by down-regulation of intestinal Niemann–Pick C1-like 1 protein (NPC1L1) and up-regulation of liver cholesterol-7α-hydroxylase (CYP7A1). We concluded that soybean germ oil favorably modulated the blood cholesterol concentration by inhibiting cholesterol absorption through inhibiting gene expression of NPC1L1 and by enhancing bile acid excretion via promoting gene expression of CYP7A1.